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PubMed2002

Field and laboratory investigations of inactivation of viruses (PRD1 and MS2) attached to iron oxide-coated quartz sand.

Field and laboratory experiments were conducted to investigate inactivation of viruses attached to mineral surfaces. In a natural gradient transport field experiment, bacteriophage PRD1, radiolabeled with 32P, was injected into a ferric oxyhydroxide-coated sand aquifer with bromide and linear alkylbenzene sulfonates. In a zone of the aquifer contaminated by secondary sewage infiltration, small fractions of infective and 32P-labeled PRD1 broke through with the bromide tracer,followed bythe slow release of 84% of the 32P activity and only 0.011% of the infective PRD1. In the laboratory experiments, the inactivation of PRD1, labeled with 35S (protein capsid), and MS2, dual radiolabeled with 35S (protein capsid) and 32P (nucleic acid), was monitored in the presence of groundwater and sediment from the contaminated zone of the field site. Release of infective viruses decreased at a much faster rate than release of the radiolabels, indicating that attached viruses were undergoing surface inactivation. Disparities between 32P and 35S release suggest that the inactivated viruses were released in a disintegrated state. Comparison of estimated solution and surface inactivation rates indicates solution inactivation is approximately 3 times as fast as surface inactivation. The actual rate of surface inactivation may be substantially underestimated owing to slow release of inactivated viruses.

Bacteriophage PRD1↗
PubMed2003

Synthesis of a single four-ring (S4R) molecular zinc phosphate and its assembly to an extended polymeric structure: a single-crystal and in-situ MAS NMR investigation.

A reaction of ZnO, HCl, H(3)PO(4), and 2-pyridylpiperazine in THF/H(2)O mixture at 75 degrees C for 72 h produces a new zinc phosphate, [(C(5)NH(5))(C(4)N(2)H(10))][Zn(H(2)PO(4))(2)(HPO(4))], I. Zinc phosphate I consists of single four-ring (S4R) units with terminal phosphoryl groups hanging from the Zn center. On reaction with zinc acetate dihydrate in the presence of water at 100 degrees C, I gave another new zinc phosphate, [(C(5)NH(5))(C(4)N(2)H(10))][Zn(2)(H(2)PO(4))(HPO(4))(PO(4))] x 2H(2)O, II. II has a layer structure with apertures formed by 4- and 8-T atoms (T = Zn, P). An examination of the two structures reveals that I and II are related, II being formed by the direct addition of Zn(2+) ions to I. Room-temperature (31)P MAS NMR studies show the presence of different phosphorus species in both compounds. An in-situ (31)P MAS NMR investigation on the formation of II from I in the presence of Zn(2+) ions and water reveals the transformation to be facile. What is noteworthy in this study is that the structural integrity of the S4Rs has been maintained during the formation of II. Donor-acceptor hydrogen bond interactions and pi-pi interactions involving the pyridyl groups also appear to play subtle roles in both phosphates. This study, the first attempt of its kind, combines the principles of supramolecular organic chemistry with inorganic building units and contributes to our understanding of the formation of framework solids.

Journal Article↗
PubMed2004

Versatile 5'-functionalization of oligonucleotides on solid support: amines, azides, thiols, and thioethers via phosphorus chemistry.

Although the preparation of conjugates of oligonucleotides is by now commonplace, existing methods (usually utilizing thiols or primary amines) are generally expensive, and often require postsynthetic reaction with the DNA followed by a separate purification. Here we describe simple procedures for a broad set of direct 5'-end (5'-terminal carbon) functionalizations of DNA oligonucleotides while they remain on the synthesizer column. 5'-Iodinated oligonucleotides (prepared by an automated cycle as previously reported) are converted directly to 5'-azides, 5'-thiocarbamates, and alkyl and aryl 5'-thioethers in high yields. Further, we demonstrate high-yielding conversions of DNA-azides to 5'-amines, and of thiocarbamates to 5'-thiols. Finally, we report a new, one-pot conversion of naturally substituted 5'-OH oligonucleotides (again on the solid support) to 5'-amino-oligonucleotides. All of the above reactions are demonstrated in multiple sequence contexts. Most of the procedures are automatable.

Amines↗
PubMed2006

Phosphonodifluoromethyl and phosphonothiodifluoromethyl radicals. Generation and addition onto alkenes and alkynes.

[reaction: see text] Selanylated difluoromethylphosphonates and difluoromethylphosphonothioates are good precursors to phosphonodifluoromethyl and phosphonothiodifluoromethyl radicals, respectively. When generated in the presence of alkenes and a hydrogen donor, the corresponding alpha,alpha-difluorinated alkylphosphonates or alkylphosphonothioates are produced in fair to good yields. The use of alkynes results in the formation of alpha,alpha-difluorinated allyl derivatives in useful yields. The presence of the sulfur atom in phosphonothiodifluoromethyl radicals usually translates into higher isolated yields.

Alkenes↗
PubMed2006

Solid-phase synthesis of dinucleoside and nucleoside-carbohydrate phosphodiesters and thiophosphodiesters.

Unprotected nucleosides (ROH) were reacted with two polymers bound to N,N-diisopropylamino-1,3,2-oxathiaphospholane in the presence of 1H-terazole. Oxidation with tert-butyl hydroperoxide or sulfurization with Beaucage's reagent, followed by the 1,3,2-oxathiaphospholane ring opening with unprotected nucleosides or carbohydrates (R'OH) in the presence of DBU, afforded nucleoside-(5'-5')-nucleoside or nucleoside-carbohydrate phosphodiester and thiophosphodiester derivatives through the elimination of polymer-bound ethylene episulfide. This strategy offers the advantages of facile isolation of final products and monosubstitution of unprotected nucleosides and carbohydrates.

Carbohydrates↗

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